Engineering Commons^™

Triphlapan: Predicting Hla Molecules Binding Peptides Based On Triple Coding Matrix And Transfer Learning, Meng Wang, Chuqi Lei, Jianxin Wang, Yaohang Li, Min Li

Computer Science Faculty Publications

Human leukocyte antigen (HLA) recognizes foreign threats and triggers immune responses by presenting peptides to T cells. Computationally modeling the binding patterns between peptide and HLA is very important for the development of tumor vaccines. However, it is still a big challenge to accurately predict HLA molecules binding peptides. In this paper, we develop a new model TripHLApan for predicting HLA molecules binding peptides by integrating triple coding matrix, BiGRU + Attention models, and transfer learning strategy. We have found the main interaction site regions between HLA molecules and peptides, as well as the correlation between HLA encoding and binding …

Microfabrication Of Silicon Carbide And Metallized Polymers Using A Femtosecond Laser, Joseph Taylor Eddy

Theses and Dissertations

Femtosecond lasers deliver a high peak concentration of optical power while maintaining low average power. With an accompanying optical setup, this power can be focused and used for high-precision fabrication of metallized polymers via ablation, creating conductive structures on a thin film. These lasers can also be harnessed in tandem with hydrofluoric acid and the two-photon absorption principle to selectively etch silicon carbide, a very durable and machining-resistant semiconductor with desirable properties. This thesis presents improvements made to the Laser-Assisted Chemical Etching (LACE) technique and the ablation system. ��, the two- photon absorption coefficient of silicon carbide, is measured and …

Identification Of Proteins Involved In Cell Membrane Permeabilization By Nanosecond Electric Pulses (Nsep), Giedre Silkuniene, Uma Mangalanathan, Alessandra Rossi, Peter A. Mollica, Andrei G. Pakhomov, Olga N. Pakhomova

Bioelectrics Publications

The study was aimed at identifying endogenous proteins which assist or impede the permeabilized state in the cell membrane disrupted by nsEP (20 or 40 pulses, 300 ns width, 7 kV/cm). We employed a LentiArray CRISPR library to generate knockouts (KOs) of 316 genes encoding for membrane proteins in U937 human monocytes stably expressing Cas9 nuclease. The extent of membrane permeabilization by nsEP was measured by the uptake of Yo-Pro-1 (YP) dye and compared to sham-exposed KOs and control cells transduced with a non-targeting (scrambled) gRNA. Only two KOs, for SCNN1A and CLCA1 genes, showed a statistically significant reduction in …

Ultra-Low Intensity Post-Pulse Affects Cellular Responses Caused By Nanosecond Pulsed Electric Fields, Kamal Asadipour, Carol Zhou, Vincent Yi, Stephen J. Beebe, Shu Xiao

Electrical & Computer Engineering Faculty Publications

High-intensity nanosecond pulse electric fields (nsPEF) can preferentially induce various effects, most notably regulated cell death and tumor elimination. These effects have almost exclusively been shown to be associated with nsPEF waveforms defined by pulse duration, rise time, amplitude (electric field), and pulse number. Other factors, such as low-intensity post-pulse waveform, have been completely overlooked. In this study, we show that post-pulse waveforms can alter the cell responses produced by the primary pulse waveform and can even elicit unique cellular responses, despite the primary pulse waveform being nearly identical. We employed two commonly used pulse generator designs, namely the Blumlein …

Abbott Cardiac Electrophysiology Wet Lab Project, Melissa Kurani, Fiona Lynn

Biomedical Engineering: Graduate Reports and Projects

Cardiac mapping systems provide electrophysiologists with pertinent information about ablation treatment plans for patients who suffer from cardiac arrhythmias. This thesis describes the process of designing a functional wet lab that integrates with Abbott’s EnSite Precision 3D Mapping System, with the purpose of providing Cal Poly students and faculty with an opportunity to have a hands-on learning experience with cardiac mapping. This project encompassed a thorough literature review of cardiology, electrophysiology, and in vitro lab systems, followed by the design, manufacturing, and evaluation of a functional and anatomically representative wet lab. This is a continuation of previous master’s projects that …

A Decoupled Engineering Methodology For Accurate Prediction Of Ablative Surface Boundary Conditions In Thermal Protection Systems, Justin Cooper

Theses and Dissertations--Mechanical Engineering

The main objective of the present work is to demonstrate a method for prediction of aerothermal environments in the engineering design of hypersonic vehicles as an alternative to the current heritage method. Flat plate and stagnation point boundary layer theory require multiple assumptions to establish the current engineering paradigm. Chief among these assumptions is the similarity between mass and heat transfer. Origins of these assumptions are demonstrated and their relationship to conservative engineering design is analyzed, as well as conditions where they possibly break down. An alternative approach for assessing aerothermal environments from the fluid domain is presented, which permits …

Kentucky Re-Entry Universal Payload System (Krups): Hypersonic Re-Entry Flight, John Daniel Schmidt

Theses and Dissertations--Mechanical Engineering

The Kentucky Re-entry Universal Payload System (KRUPS) is a small capsule designed as a technology testbed for re-entry experiments. For its first incarnation, KRUPS has been designed to test Thermal Protection Systems (TPS) and instruments in re-entry flights. Because of the unique environment a vehicle undergoes during re-entry, there is a high-demand for experimental data from re-entry experiments. KRUPS has been developed at the University of Kentucky (UK) over the past seven years to meet this demand. After completing sub-orbital campaigns, the first KRUPS hypersonic re-entry mission was attempted. The mission involved building three 11-inch diameter capsules each outfitted with …

Numerical Investigation On The Effect Of Spectral Radiative Heat Transfer Within An Ablative Material, Raghava S. C. Davuluri, Rui Fu, Kaveh A. Tagavi, Alexandre Martin

Mechanical Engineering Faculty Publications

The spectral radiative heat flux could impact the material response. In order to evaluate it, a coupling scheme between KATS - MR and P1 approximation model of radiation transfer equation (RTE) is constructed and used. A Band model is developed that divides the spectral domain into small bands of unequal widths. Two verification studies are conducted: one by comparing the simulation computed by the Band model with pure conduction results and the other by comparing with similar models of RTE. The comparative results from the verification studies indicate that the Band model is computationally efficient and can be used to …

Modeling Thin Layers In Material Response Solvers, Christen Setters

Theses and Dissertations--Mechanical Engineering

Thermal Protection Systems (TPS) are a necessary component for atmospheric entry. Most TPS contain thin layers of various materials such as ceramic coatings, pore sealers and bonding agents. When modeling TPS, these thin layers are often neglected due to the difference in scale between the TPS (centimeters) and the thin layers (micrometers). In this study, a volume-averaging flux-conservation method is implemented in the governing equations of a finite volume material response code. The model proposes the addition of a volume and area fraction coefficient which utilizes a weighted-averaging between the amount of thin layer and heat shield material in a …

Laser Micropatterning Effects On Corrosion Resistance Of Pure Magnesium Surfaces, Yahya Efe Yayoglu

USF Tampa Graduate Theses and Dissertations

Magnesium and its alloys are good candidates to manufacture medical implants. They have excellent biocompatibility and because they biodegrade secondary surgical operation to remove the implant could be eliminated. However, in aqueous environments, magnesium alloys rapidly corrode, resulting in premature degradation of the implant along with biologically intolerable hydrogen gas generation. In literature, there are multiple studies focused on creating water repelling hydrophobic magnesium surfaces in order to decrease corrosion rates. Hydrophobic properties can be achieved by creation of a roughness profile on an initially smooth surface combined with a treatment that reduces the free surface energy. In theory, hydrophobic …

Impedance Analysis Of Tissues In Nspef Treatment For Cancer Therapy, Edwin Ayobami Oshin

Biomedical Engineering Theses & Dissertations

Nanosecond pulsed electric field (nsPEF) for cancer therapy is characterized by applications of high voltage pulses with low pulsed energy to induce non-thermal effects on tissues such as tumor ablation. It nonthermally treats tissues via electroporation. Electroporation is the increase in permeabilization of a cell membrane due to the application of high pulsed electric field. The objective of this study was to investigate the effect of nsPEF on tissue by monitoring the tissue’s impedance in real-time. Potato slices (both untreated and electroporated), and tumors extracted from female BALBc mice were studied. 100ns, 1-10kV pulses were applied to the tissues using …

Laser Induced Thermal Degradation Of Carbon Fiber-Carbon Nanotube Hybrid Laminates, Joshua A. Key

Theses and Dissertations

Recent advancements in fiber laser technology have increased interest in target material interactions and the development of thermal protection layers for tactical laser defense. A significant material of interest is carbon fiber reinforced polymers due to their increased use in aircraft construction. In this work, the thermal response of carbon fiber-carbon nanotube (CNT) hybrid composites exposed to average irradiances of 0.87-6.8 W/cm² were observed using a FLIR sc6900 thermal camera. The camera had a pixel resolution of 640x512 which resulted in a spatial resolution of 0.394x0.383 mm/pixel for the front and 0.463x0.491 mm/pixel for the back. The hybrid samples …

Development Of Universal Solver For High Enthalpy Flows Through Ablative Materials, Umran Duzel

Theses and Dissertations--Mechanical Engineering

Atmospheric entry occurs at very high speeds which produces high temperature around the vehicle. Entry vehicles are thus equipped with Thermal Protection Systems which are usually made of ablative materials. This dissertation presents a new solver that models the atmospheric entry environment and the thermal protection systems. In this approach, both the external flow and the porous heat shield are solved using the same computational domain. The new solver uses the Volume Averaged Navier-Stokes Equations adapted for hypersonic non-equilibrium flow, and is thus valid for both domains. The code is verified using analytical problems, set of benchmarks and also a …

Metal Coupon Testing In An Axial Rotating Detonation Engine For Wear Characterization, Gary S. North

Browse all Theses and Dissertations

Rotating Detonation Engines (RDE) are being explored as a possible way to get better fuel efficiency for turbine engines than is otherwise possible. The walls of the RDE are subjected to cyclic thermal and mechanical shock loading at rates of approximately 3 KHz, with gas temperatures as high as 2976 K. This project performed testing with Inconel 625 and 304 stainless steel coupons in an RDE outer body to attempt to measure material ablation rates. Significant microstructural changes were observed to include grain growth in both alloys, carbide formation and grain boundary melting in Inconel, and formation of delta ferrite …

Investigations Of Thermal Treatment Of Softwood Kraft Lignin Under Fractional And Ablative Pyrolytic Conditions, Dideolu J. Daniel

LSU Master's Theses

Lignin is second to cellulose in abundance among polymers in nature. Research studies on the development of new products and material combinations in which lignin degradation/conversion products are involved are still in their infancy, because fundamental knowledge about its structure, reactivity, and material and polymer behavior, is still lacking.

The objective of this research study was to investigate the complex thermal deconstruction and mechanistic behavior of a type of technical lignin, known as Kraft lignin, under depolymerization and to develop operating conditions for parameters influencing resulting product yields and operation of pyrolysis reactors.

Softwood Kraft lignin (s-KL) and methanol-fractionated (ex-KL) …

Modeling Of Complex Parts For Industrial Waterjet Cleaning, Braden James

Graduate Theses and Dissertations

Industrial high-pressure waterjet cleaning is common to many industries. The modeling in this paper functions inside a collaborative robotic framework for high mix, low volume processes where human robot collaboration is beneficial. Automation of pressure washing is desirable for economic and ergonomic reasons. An automated cleaning system needs path simulation and analysis to give the operator insight into the predicted cleaning performance of the system. In this paper, ablation, the removal of a substrate coating by waterjet, is modeled for robotic cleaning operations. The model is designed to work with complex parts often found in spray cleaning operations, namely parts …

Nanosecond Pulsed Electric Fields Induce Endoplasmic Reticulum Stress Accompanied By Immunogenic Cell Death In Murine Models Of Lymphoma And Colorectal Cancer, Alessandra Rossi, Olga N. Pakhomova, Peter A. Mollica, Maura Casciola, Uma Mangalanathan, Andrei G. Pakhomov, Claudia Muratori

Bioelectrics Publications

Depending on the initiating stimulus, cancer cell death can be immunogenic or non-immunogenic. Inducers of immunogenic cell death (ICD) rely on endoplasmic reticulum (ER) stress for the trafficking of danger signals such as calreticulin (CRT) and ATP. We found that nanosecond pulsed electric fields (nsPEF), an emerging new modality for tumor ablation, cause the activation of the ER-resident stress sensor PERK in both CT-26 colon carcinoma and EL-4 lymphoma cells. PERK activation correlates with sustained CRT exposure on the cell plasma membrane and apoptosis induction in both nsPEF-treated cell lines. Our results show that, in CT-26 cells, the activity of …

Experimental And Computational Analysis Of The Interaction Of Carbon And Silicon Ablation Products In Expanding Hypersonic Flows, Brian E. Donegan

Theses and Dissertations

Thermal protection is required for vehicles entering planetary atmospheres to protect against the severe heating loads experienced. Characterization of candidate materials is often done utilizing plasma or arc-jet facilities, which provide steady-state testing of the thermal environments experienced during hypersonic flight, but do not correctly simulate hypersonic flowfields. Conversely, impulse facilities can reproduce flight velocities and enthalpies but have extremely short test times, prohibiting testing of thermal response. Modeling ablation and heating rates, particularly in the wake region, remains a significant challenge due to the complexity of the flowfield. To better understand this complex phenomenon and provide data to validate …

Moderate Heat Application Enhances The Efficacy Of Nanosecond Pulse Stimulation For The Treatment Of Squamous Cell Carcinoma, Chelsea M. Edelblute, Sigi Guo, Embo Yang, Chunqi Jiang, Karl Schoenbach, Richard Heller

Bioelectrics Publications

Nanosecond pulse stimulation as a tumor ablation therapy has been studied for the treatment of various carcinomas in animal models and has shown a significant survival benefit. In the current study, we found that moderate heating at 43°C for 2 minutes significantly enhanced in vitro nanosecond pulse stimulation-induced cell death of KLN205 murine squamous cell carcinoma cells by 2.43-fold at 600 V and by 2.32-fold at 900 V, as evidenced by propidium iodide uptake. Furthermore, the ablation zone in KLN205 cells placed in a 3-dimensional cell-culture model and pulsed at a voltage of 900 V at 43°C was 3 times …

Limits Of Existence Of The State Layer By Liquefaction Of Heterogeneous Mixture “Solid Body-Solid Body”., A.Sh Abdullaev, N.A Annaev, Kh.S Nurmuhamedov, S.K Nigmadjanov

Chemical Technology, Control and Management

In article are considered a status of layers for the systems "solid body-solid body" in case of liquefaction in the liquid environment when superimposing a gas flow and also critical speeds of a three-phase fluidized layer. The experimental data on the speed of the beginning of pseudo-liquefaction of Reps and ablation of Reab of bodies of irregular shape are generalized in the form of criteria formulas. Results on critical speeds slightly differ from the received estimated formulas. The received formulas describe boundaries of transition of statuses of a layer in a broad range of change of the equivalent diameter of …

Calculation Of The Rate Of Entrainment In Three-Phase Fluidization With Solid Non-Uniform Mixtures, A.Sh Abdullaev, O.Sh Temirov, Kh.S Nurmuhamedov

Chemical Technology, Control and Management

Article is devoted to determination of critical speeds of a compound from solid bodies with sharply different physicomechanical properties in a three-phase fluidized layer. Critical speeds, in particular, the speed of ablation of wab of a thin skin of root crops, in the form of a thin plate of irregular shape are defined. Results on critical speed of ablation considerably differ from the estimated values received on a formula Todes O.M. Therefore, for increase in accuracy of determination of critical speed of ablation of a three-phase fluidized layer the correlation considering a factor of the form and sailing of bodies …

Nano-Pulse Stimulation For The Treatment Of Pancreatic Cancer And The Changes In Immune Profile, Sigi Guo, Niculina I. Burcus, James Hornef, Yu Jing, Chunqi Jiang, Richard Heller, Stephen J. Beebe

Bioelectrics Publications

A Pancreatic cancer is a notorious malignant neoplasm with an extremely poor prognosis. Current standard of care is rarely effective against late-stage pancreatic cancer. In this study, we assessed nanopulse stimulation (NPS) as a local treatment for pancreatic cancer in a syngeneic mouse Pan02 pancreatic cancer model and characterized corresponding changes in the immune profile. A single NPS treatment either achieved complete tumor regression or prolonged overall survival in animals with partial tumor regression. While this is very encouraging, we also explored if this local ablation effect could also result in immune stimulation, as was observed when NPS led to …

Thermo-Mechanical Coupling For Ablation, Rui Fu

Theses and Dissertations--Mechanical Engineering

In order to investigate the thermal stress and expansion as well as the associated strain effect on material properties caused by high temperature and large temperature gradient, a two-way thermo-mechanical coupling solver is developed. This solver integrates a new structural response module to the Kentucky Aerothermodynamics and Thermal response System (KATS) framework. The structural solver uses a finite volume approach to solve either hyperbolic equations for transient solid mechanics, or elliptic equations for static solid mechanics. Then, based on the same framework, a quasi-static approach is used to couple the structural response and thermal response to estimate the thermal expansion …

Verification And Validation Studies For The Kats Aerothermodynamics And Material Response Solver, Olivia Schroeder

Theses and Dissertations--Mechanical Engineering

Modeling the atmospheric entry of spacecraft is challenging because of the large number of physical phenomena that occur during the process. In order to study thermal protection systems, engineers rely on high fidelity solvers to provide accurate predictions of both the thermochemical environment surrounding the heat shield, and its material response. Therefore, it is necessary to guarantee that the numerical models are correctly implemented and thoroughly validated. In recent years, a high-fidelity modeling tool has been developed at the University of Kentucky for the purpose of studying atmospheric entry. The objective of this work is to verify and validate this …

Delayed Hypersensitivity To Nanosecond Pulsed Electric Field In Electroporated Cells, Sarah D. Jensen, Vera A. Khorokhorina, Claudia Muratori, Andrei G. Pakhomov, Olga N. Pakhomova

Bioelectrics Publications

We demonstrate that conditioning of mammalian cells by electroporation with nanosecond pulsed electric field (nsPEF) facilitates their response to the next nsPEF treatment. The experiments were designed to unambiguously separate the electroporation-induced sensitization and desensitization effects. Electroporation was achieved by bursts of 300-ns, 9 kV/cm pulses (50 Hz, n = 3–100) and quantified by propidium dye uptake within 11 min after the nsPEF exposure. We observed either sensitization to nsPEF or no change (when the conditioning was either too weak or too intense, or when the wait time after conditioning was too short). Within studied limits, conditioning never caused desensitization. …

Controllable Moderate Heating Enhances The Therapeutic Efficacy Of Irreversible Electroporation For Pancreatic Cancer, Chelsea M. Edelblute, James Hornef, Niculina I. Burcus, Thomas Norman, Stephen J. Beebe, Karl Schoenbach, Richard Heller, Chunqi Jiang, Sigi Guo

Bioelectrics Publications

Irreversible electroporation (IRE) as a non-thermal tumor ablation technology has been studied for the treatment of pancreatic carcinoma and has shown a significant survival benefit. We discovered that moderate heating (MH) at 43°C for 1-2 minutes significantly enhanced ex vivo IRE tumor ablation of Pan02 cells by 5.67-fold at 750 V/cm and by 1.67-fold at 1500 V/cm. This amount of heating alone did not cause cell death. An integrated IRE system with controllable laser heating and tumor impedance monitoring was developed to treat mouse ectopic pancreatic cancer. With this novel IRE system, we were able to heat and maintain the …

Steady State Simulation Of Pyrolysis Gases In An Inductively Coupled Plasma Facility, Nicholas C. Martin

Graduate College Dissertations and Theses

An important step in the more efficient use of PICA (Phenolic Impregnated Carbon Ablator) as a Thermal Protection System (TPS) material for spacecraft is the understanding of its pyrolysis mechanics. The gases released during pyrolysis and their subsequent interaction with the reactive plasma environment is not yet well understood. The surface recession of PICA as it ablates during testing only makes the study and characterization of the chemical reactions more difficult. To this end, a probe has been designed for this study to simulate, in steady state, the pyrolysis gases within the UVM 30kW Inductively Coupled Plasma (ICP) Torch Facility. …

Investigation Of Pyrolysis Gas Chemistry In An Inductively Coupled Plasma Facility, Corey Tillson

Graduate College Dissertations and Theses

The pyrolysis mechanics of Phenolic Impregnated Carbon Ablators (PICA) makes it a valued material for use in thermal protection systems for spacecraft atmospheric re-entry. The present study of the interaction of pyrolysis gases and char with plasma gases in the boundary layer over PICA and its substrate, FiberForm, extends previous work on this topic that has been done in the UVM 30 kW Inductively Coupled Plasma (ICP) Torch Facility. Exposure of these material samples separately to argon, nitrogen, oxygen, air, and carbon dioxide plasmas, and combinations of said test gases provides insight into the evolution of the pyrolysis gases as …

Development Of Inverse Methods For Reconstruction Of Flight Environments On Ablators, A. Brandon Oliver

Open Access Dissertations

Obtaining measurements of flight environments on ablative heatshields is both critical for spacecraft development and extremely challenging due to the harsh heating environment and surface recession. Thermocouples installed several millimeters below the surface are commonly used to measure the heatshield temperature response, but an ill-posed inverse heat conduction problem must be solved to reconstruct the surface heating environment from the embedded thermocouple measurements. The material properties of typical ablators make the reconstruction process more challenging when the measurements are deep, but measurements often must be located deep to allow for surface recession. Compounding the complexity of the surface reconstruction problem, …

A Mechanistically Guided Approach To Treatment Of Multi-Wavelet Reentry: Experiments In A Computational Model Of Cardiac Propagation, Richard T. Carrick

Graduate College Dissertations and Theses

Atrial fibrillation (AF) is the most common cardiac arrhythmia in the United States today. However, treatment options remain limited despite the enormous magnitude of both AF prevalence and the associated economic cost. Of those treatment options that are available, ablation-based interventional methods have demonstrated the highest rates of long-term cure. Unfortunately, these methods have substantially lower efficacy in patients with heavier burdens of disease, thus leaving the most affected individuals with the least hope for successful treatment.

The focus of this research is to develop a mechanistically guided approach towards the treatment of multi-wavelet reentry (MWR), one of the primary …